Physically-Based Droplet Interaction

In this paper we present a physically-based model for simulating realistic interactions between liquid droplets in an efficient manner. Our particle-based system recreates the coalescence, separation and fragmentation interactions that occur between colliding liquid droplets and allows systems of droplets to be meaningfully repre- sented by an equivalent number of simulated particles. By consid- ering the interactions specific to liquid droplet phenomena directly, we display novel levels of detail that cannot be captured using other interaction models at a similar scale. Our work combines experi- mentally validated components, originating in engineering, with a collection of novel modifications to create a particle-based interac- tion model for use in the development of mid-to-large scale droplet- based liquid spray effects. We demonstrate this model, alongside a size-dependent drag force, as an extension to a commonly-used ballistic particle system and show how the introduction of these interactions improves the quality and variety of results possible in recreating liquid droplets and sprays, even using these otherwise simple systems

An Allosteric Inhibitor of KRas Identified Using a Barcoded Rapid Assay Microchip Platform

Protein catalyzed capture agents (PCCs) are synthetic antibody surrogates that can target a wide variety of biologically relevant proteins. As a step toward developing a high-throughput PCC pipeline, we report on the preparation of a barcoded rapid assay platform for the analysis of hits from PCC library screens. The platform is constructed by first surface patterning a micrometer scale barcode composed of orthogonal ssDNA strands onto a glass slide. The slide is then partitioned into microwells, each of which contains multiple copies of the full barcode. Biotinylated candidate PCCs from a click screen are assembled onto the barcode stripes using a complementary ssDNA-encoded cysteine-modified streptavidin library. This platform was employed to evaluate candidate PCC ligands identified from an epitope targeted in situ click screen against the two conserved allosteric switch regions of the Kirsten rat sarcoma (KRas) protein. A single microchip was utilized for the simultaneous evaluation of 15 PCC candidate fractions under more than a dozen different assay conditions. The platform also permitted more than a 10-fold savings in time and a more than 100-fold reduction in biological and chemical reagents relative to traditional multiwell plate assays. The best ligand was shown to exhibit an in vitro inhibition constant (IC_(50)) of ∼24 μM

Wave curves: Simulating Lagrangian water waves on dynamically deforming surfaces

We propose a method to enhance the visual detail of a water surface simulation. Our method works as a post-processing step which takes a simulation as input and increases its apparent resolution by simulating many detailed Lagrangian water waves on top of it. We extend linear water wave theory to work in non-planar domains which deform over time, and we discretize the theory using Lagrangian wave packets attached to spline curves. The method is numerically stable and trivially parallelizable, and it produces high frequency ripples with dispersive wave-like behaviors customized to the underlying fluid simulation

Origin and history of Phoxinus (Cyprinidae) introductions in the Douro basin (Iberian Peninsula): an update inferred from genetic data

The number of non-native freshwater fishes in the Iberian Peninsula has been greatly increasing. In this study, individuals of the genus Phoxinus were detected in 18 out of 138 stream sites sampled across the Douro Basin in 2017 and 2018. A total of 26 individuals were barcoded using partial cytochrome c oxidase subunit I (COI) and cytochrome b (cytb) genes for species identification and determination of geographical origin. Molecular data provided the first record of a second Phoxinus species in western Douro (Portugal, Iberian Peninsula), with haplotypes closely matching those found in the Charente River (southern France). This species is suspected to be a recent introduction associated with the use of minnows as live bait by freshwater anglers, which was facilitated by human movements between France and Portugal. Individuals from watercourses in eastern Douro (Spain) were genetically assigned to Phoxinus bigerri, an introduced species previously known for that region, which confirms reports of introduction events from Ebro to Douro Basin probably also related to freshwater angling and facilitated by geographic proximity. The potential ecological impacts of this genus in the region are unknown and need further investigation.We acknowledge Fernando Teixeira, Fernando Miranda, Mario Ferreira, Sara Carona, Jose Pedro RamiAo and Francisco Carvalho for the valuable assistance during fieldwork. We specially thank Maria Filomena MagalhAes for previous fruitful discussions and logistic support. We are grateful to Matthias F. Geiger and Andrea Corral Lou for facilitating genetic data and coordinates of sampling sites. Finally, we appreciate the comments of the three anonymous reviewers that improved the quality of the manuscript. AFF and AGR were supported by the project FRESHING founded by the Portuguese Foundation for Science and Technology (FCT) and COMPETE (PTDC/AAGMAA/2261/2014 - POCI-01-0145-FEDER-356016824). FMSM was supported by the FCT PhD grant SFRH/BD/104703/2014. This study was conducted as part of the projects FRESHING and FRESHCO. The latter is also supported by FCT and COMPETE (PTDC/AGR-FOR/1627/2014 - 04/SAICT/2015) and UID/AGR/04033/2019. Logistic support was also facilitated by the ENVMETAGEN - Capacity Building at InBIO for Research and Innovation Using Environmental Metagenomics project at CIBIO laboratories (668981; EUH2020-WIDESPREAD-2014-2)

An Allosteric Inhibitor of KRas Identified Using a Barcoded Rapid Assay Microchip Platform

Protein catalyzed capture agents (PCCs) are synthetic antibody surrogates that can target a wide variety of biologically relevant proteins. As a step toward developing a high-throughput PCC pipeline, we report on the preparation of a barcoded rapid assay platform for the analysis of hits from PCC library screens. The platform is constructed by first surface patterning a micrometer scale barcode composed of orthogonal ssDNA strands onto a glass slide. The slide is then partitioned into microwells, each of which contains multiple copies of the full barcode. Biotinylated candidate PCCs from a click screen are assembled onto the barcode stripes using a complementary ssDNA-encoded cysteine-modified streptavidin library. This platform was employed to evaluate candidate PCC ligands identified from an epitope targeted in situ click screen against the two conserved allosteric switch regions of the Kirsten rat sarcoma (KRas) protein. A single microchip was utilized for the simultaneous evaluation of 15 PCC candidate fractions under more than a dozen different assay conditions. The platform also permitted more than a 10-fold savings in time and a more than 100-fold reduction in biological and chemical reagents relative to traditional multiwell plate assays. The best ligand was shown to exhibit an in vitro inhibition constant (IC_(50)) of ∼24 μM

Tryptophan-Accelerated Electron Flow Through Proteins

Energy flow in biological structures often requires submillisecond charge transport over long molecular distances. Kinetics modeling suggests that charge-transfer rates can be greatly enhanced by multistep electron tunneling in which redox-active amino acid side chains act as intermediate donors or acceptors. We report transient optical and infrared spectroscopic experiments that quantify the extent to which an intervening tryptophan residue can facilitate electron transfer between distant metal redox centers in a mutant Pseudomonas aeruginosa azurin. CuI oxidation by a photoexcited ReI-diimine at position 124 on a histidine(124)-glycine(123)-tryptophan(122)-methionine(121) β strand occurs in a few nanoseconds, fully two orders of magnitude faster than documented for single-step electron tunneling at a 19 angstrom donor-acceptor distance

Why Should We Preserve Fishless High Mountain Lakes?

High mountain lakes are originally fishless, although many have had introductions of non-native fish species, predominantly trout, and recently also minnows introduced by fishermen that use them as live bait. The extent of these introductions is general and substantial often involving many lakes over mountain ranges. Predation on native fauna by introduced fish involves profound ecological changes since fish occupy a higher trophic level that was previously inexistent. Fish predation produces a drastic reduction or elimination of autochthonous animal groups, such as amphibians and large macroinvertebrates in the littoral, and crustaceans in the plankton. These strong effects raise concerns for the conservation of high mountain lakes. In terms of individual species, those adapted to live in larger lakes have suffered a higher decrease in the size of their metapopulation. This ecological problem is discussed from a European perspective providing examples from two study areas: the Pyrenees and the Western Italian Alps. Species-specific studies are urgently needed to evaluate the conservation status of the more impacted species, together with conservation measures at continental and regional scales, through regulation, and at local scale, through restoration actions, aimed to stop further invasive species expansions and to restore the present situation. At different high mountain areas of the world, there have been restoration projects aiming to return lakes to their native fish-free status. In these areas autochthonous species that disappeared with the introduction of fish are progressively recovering their initial distribution when nearby fish-free lakes and ponds are available

Flensjøen i kommunene Os og Røros 2012. Status for vannkvalitet og biologiske forhold etter kalking siden 2005

Rapporten omhandler vannkvalitet og biologiske forhold inklusive fisk i Flensjøen etter kalking. Innsjøens vannkvalitet viste bedring fra 1970- og 1980-tallet og fram til 2005, før kalking. Kalkingen har bidratt til en ytterligere bedring av vannkvaliteten i form av økt pH og ANC. Flensjøens vannkjemi er trolig i seg selv ikke begrensende for fiskebestandene, og vil muligens heller ikke være det uten kalking. Hvorvidt gytebekker for ørreten har tilfredsstillende vannkvalitet, er ikke undersøkt. Lave konsentrasjoner av total-fosfor og total-nitrogen samt lav biomasse av krepsdyrplankton i 2005-2012 indikerte næringsfattige forhold. Krepsdyrplanktonet og samfunnet av litorale småkreps har vært dominert av forsuringstolerante arter, men et mindre antall forsurings-følsomme arter har også blitt registrert både før og etter kalking. Undersøkelsene av bunndyr i utløpselva i 2005-2012 indikerte en økning i biologisk mangfold uttrykt ved EPT etter kalking. Økologisk tilstand mht. effekter av forsuring på bunndyrsamfunnene viste en bedring fra moderat tilstand i 2005 til svært god tilstand i 2006-2012. Sammenlignet med undersøkelsene i 2006/2007 synes det som at ørretbestanden er noe tettere. Veksten er imidlertid relativt lik som tidligere, og kondisjonsfaktoren er moderat for større fisk. Røyebestanden besto av flere eldre og større fisk i 2012 enn i 2006/07, og veksten syntes også å ha bedret seg siden de forrige undersøkelsene. Selv om flere faktorer kan spille inn, er det er sannsynlig at kalkingen har hatt en positiv effekt på fiskebestandene